A Comprehensive Analysis of the PI3K/AKT Pathway: Unveiling Key Proteins and Therapeutic Targets for Cancer Treatment

Abstract

Background:

Cancer development and progression involve a complex network of pathways among which certain pathways play a pivotal role in promoting tumor growth and survival. An important pathway in this context is the PI3K/AKT pathway, which regulates crucial cellular processes including proliferation, viability, and metabolic regulation. Dysregulation of this pathway has been strongly linked to the development of various types of cancers. Consequently, it is imperative to identify the key proteins within this pathway as potential targets for impeding cancer cell proliferation and survival.

Results:

One of the key findings of this study was the identification of signaling proteins that dominate various forms of PI3K/Akt pathway. Furthermore, proteins play critical roles in cancer networks, acting as oncogenes that promote cancer development or as tumor suppressor genes that inhibit tumor growth. This study identified several genes, including KIT, ERBB2, PDGFRA, MET, FGFR2, and FGFR3, which are involved in various types of the PI3K/Akt pathways. Additionally, this study identified 55 proteins that are commonly found in various forms of PI3K/Akt, and these proteins play crucial roles in regulating various biological functions.

Conclusions:

This study highlights the importance of identifying key proteins involved in the PI3K/AKT pathway. In this study, we identified several genes involved in different pathways that play essential roles in the activation, signaling, and regulation of the pathway. Understanding the proteins participating in the PI3K/AKT pathway is vital for the development of targeted therapies, not only for cancer but also for other related diseases. By elucidating their roles and functions, this study contributes to the advancement of knowledge in the field and paves the way for the development of effective treatments targeting this pathway.

Introduction

Cancer is an intricate condition characterized by changes in numerous genetic pathways; that significantly affect cell growth, proliferation, and survival. A crucial pathway implicated in cancer is PI3K/AKT. ¹ This pathway plays a vital role in regulating diverse cellular processes, including metabolism, cell growth, and differentiation. ² The disruption of the normal functioning of this pathway is closely linked to the onset and progression of various cancer types. Consequently, comprehending the molecular mechanisms that underlie the PI3K/AKT pathway assumed paramount importance in the development of targeted therapies aimed at combating cancer.

Various genetic mutations and modifications in the PI3K/AKT pathway have the potential to activate oncogenes or deactivate tumor suppressor genes, resulting in unrestricted cell growth and survival. ³ Specifically, PTEN gene mutations leading to loss of function, which encode a lipid phosphatase that negatively regulates PI3K/Akt signaling, have been implicated in various cancer types, including prostate, brain, and endometrial cancer. ⁴

The identification of proteins participating in the PI3K/Akt pathway holds the utmost importance in the development of precise therapies for treating cancer and other ailments.^{5 -8} This pathway encompasses various proteins; including PI3K, Akt, mTOR, and PTEN. Among them, Akt, a serine/threonine kinase, plays a crucial role in governing numerous cellular processes, such as glucose metabolism, cell survival, and cell cycle progression. ⁹ Furthermore, key proteins, such as KIT, ERBB2, PDGFRA, MET, FGFR2, and FGFR3, play important roles in numerous cancer-related signaling pathways, especially the PI3K/AKT pathway. Below are their respective roles and involvement in cancer therapy and related pathways. KIT is critical for cell survival, proliferation, and differentiation. Mutations in KIT are commonly observed in gastrointestinal stromal tumors (GIST) and several other cancers. ¹⁰ ERBB2 plays an important role in cell growth and survival. Monoclonal antibodies against ERBB2 have been used to treat HER2-positive breast cancer. ¹¹ PDGFRA is responsible for cell proliferation and migration. Common PDGFRA mutations are associated with certain gastrointestinal tumors and other malignancies. ¹² MET is involved in cell growth, survival, and mobility. Dysregulation of MET is associated with cancer progression and drug resistance in various types of cancer. ¹³ FGFR2 is critical for cell proliferation, differentiation, and survival. Dysregulation or mutations in FGFR2 are associated with various types of cancers such as breast, gastric, and bladder cancers. ¹⁴ FGFR3 plays important roles in cell growth, differentiation, and apoptosis. FGFR3 mutations are common in multiple myeloma and bladder cancer. ¹⁵ As these proteins are critically involved in cancer-associated signaling pathways, they are promising targets for cancer therapy. Understanding their roles and dysregulation in different types of cancer will allow researchers to develop targeted therapies to treat cancer.

Therefore, the targeting the PI3K/Akt pathway has emerged as a promising therapeutic approach for cancer treatment. A range of PI3K and Akt inhibitors have been formulated and evaluated in preclinical and clinical investigations.^{16 -19}

Hence, the objective of this study was to identify the proteins involved in the PI3K/Akt pathway and to elucidate their respective functions. Such knowledge can offer valuable insights into the mechanisms underlying cancer development and progression, paving the way for the advancement of enhanced and personalized cancer therapies in the future.

Materials and Methods

Our previous work used a specific approach in which protein-protein interactions (PPIs) were treated as a metric space and analyzed using graph theory tools. ²⁰ We modeled all PPIs as a metric space, identified the topological center of each network, and classified the remaining proteins into “zones” based on their graph-theoretical distance from the central protein. For example, zone 1 refers to proteins 1 step away from the topological center, and zone 2 refers to proteins 2 steps away. We found that proteins interacted radially through a central node, with high levels of proteins aggregated at the center of the network and low levels of proteins far from the center. We also found that the distribution of proteins from the center in specific hierarchies is biologically important. Therefore, we conclude that a strategy to formally and concisely evaluate PPIs as a metric space, with an emphasis on zones relative to the center, can reveal key differences between PPI networks expressed in normal and diseased tissues. We suggest that centrally localized proteins, especially those involved in sensory function, may be good therapeutic targets, and should be formally evaluated in future studies based on our metric space approach. Our ongoing work on possible applications of the approach detailed in our previous study suggests that the central zones of some human PPI networks are highly enriched in essential proteins and known drug targets, and that central zones show even higher enrichment, supporting the hypothesis of utility in drug target discovery.^{21 -24} Building on the extension of previous analytical studies, the current study focuses on zone 2, the most crosslinked zone enriched with proteins related to various cellular functions, such as signaling pathways, immune system responses, and blood clotting processes. and disease-related pathways.

Analysis of pathways and functional enrichment

To examine the biological significance of the various zones within the PPI network, proteins were classified based on their closeness to the central point. To identify the specific functions associated with these zones, an analysis of over-representation pathways was conducted on the protein groups associated with each zone. Several tools have been employed for the enrichment analysis of the zones, including gene set enrichment in comparative toxigenomics databases and the analysis of gene ontology terms. To determine the significance of the results, a statistical threshold of 0.01 was applied. Additionally, to assess potential functional specialization within the zones, the percentage of proteins associated with each enriched pathway was calculated.

An assessment of pathways related to oncogenes and tumor suppressor proteins

An assessment was performed to evaluate the protein expression levels of oncogenes and tumor suppressors. This evaluation leveraged data from comprehensive genomic sequencing studies to identify the enriched pathways. The analysis primarily focused on examining interactions with high scores, which revealed a recurring pattern that often involved genes that were causally linked to cancer. ²⁵

Proteins essential for cellular processes, signaling, growth, cell cycle regulation, and potential therapeutic targets

To evaluate zone 2 of the functional protein interaction network in humans, ²⁶ we identified a set of key human proteins by studying the effects of knocking out their corresponding genes in mice. ²⁷

Results

We narrowed our investigation to the 4495 proteins in zone 2 and mapped them to proteins in the KEGG pathways to identify their involvement in different pathways related to PI3K/AKT, including PI3K/AKT activation (PI3K/AKT act), PI3K/AKT signaling in cancer (PI3K/AKT sig-can), PI5P, PP2A and IER3 regulation of PI3K/AKT Signaling (PI5P, PP2A, IER3 reg. PI3K/AKT sig.), negative regulation of the PI3K/AKT network (Neg. reg. PI3K/AKT net) and CD28 dependent PI3K/Akt signaling pathways. Our objective was to gain a deeper understanding of the role of these proteins. Table 1 summarizes the identified pathways.

Table 1.

Distribution of PI3K/Akt pathway related proteins within zone 2.

Type of pathway	Number of proteins
PI3K/AKT act	89
PI3K/AKT sig-can	67
PI5P, PP2A, IER3 reg. PI3K/AKT sig	72
Neg. reg. PI3K/AKT net	77
CD28 dependent PI3K/Akt signaling	14

Distribution of essential, signaling, growth, cell cycle, MAPK cascade, positive signaling and negative signaling in PI3K/Akt pathway-related proteins within zone 2

Activation and regulation of signaling pathways play a pivotal role in the initiation and progression of cancer. Cancer cells often exhibit dysregulated signaling pathways that promote cell growth and survival. Consequently, it is crucial to target these pathways to impede their ability to thrive.^{28 -31}

As indicated in Table 2, signaling proteins demonstrated significant dominance in various forms of the PI3K/AKT pathway, accounting for 90% of the overall proportion. Positive signaling was closely followed, with a proportion of 43%. The remaining functions were as follows: essential proteins (41%), MAPK cascade (36%), cell cycle (14%), growth (11%), and negative signaling (0.1%).

Table 2.

Distribution of essential, signaling, growth, cell cycle, MAPK cascade, positive signaling and negative signaling in PI3K/AKT pathway -related proteins within zone 2.

PI3K/AKT pathway type	E	S	G	C	M	P/S	N/S
PI3K/AKT act	36 (40.4%)	80 (89.9%)	11 (16.7%)	13 (12.3%)	32 (36%)	37 (25%)	12 (41.5%)
PI3K/AKT sig-can	33 (49.2%)	63 (94%)	7 (10.4%)	8 (11.9%)	26 (38.8%)	31 (46.2%)	8 (11.9%)
PI5P, PP2A, IER3 reg. PI3K/AKT sig	28 (38.8%)	63 (87.5%)	9 (12.5%)	11 (15.2%)	28 (38.8%)	32 (44.4%)	7 (9.7%)
Neg. reg. PI3K/AKT net	31 (40.2%)	68 (88.3%)	9 (11.6%)	12 (15.5%)	29 (37.6%)	33 (42.8%)	8 (10.3%)
CD28 dependent PI3K/Akt signaling	2 (14.2%)	14 (100%)	0 (0.0%)	1 (7.1%)	1 (7.1%)	4 (28.5%)	1 (7.1%)
Average percentage	130 (41%)	288 (90%)	36 (11%)	45 (14%)	116 (36%)	137 (43%)	36 (0.1%)

Abbreviations: E, essential; S, signalling; G, growth; C, cell cycle; M, MAPK cascade; P/S, positive signaling; N/S, negative signaling.

Distribution of apoptosis, positive apoptosis, negative apoptosis, oncogenes tumor suppressor, and successful therapeutic target in PI3K/Akt pathway-related proteins within zone 2

Proteins play crucial roles in cancer networks and serve as either oncogenes that promote cancer development or as tumor suppressor genes that inhibit tumor growth. The interactions between these proteins greatly affect the behavior of cancer cells.^32,33 An important signaling pathway involved in cell growth, survival, and metabolism is the PI3K/Akt pathway. It plays a significant role in maintaining the balance between cell proliferation and death. Dysregulation of this pathway may contribute to cancer onset. The PI3K/Akt pathway encompasses several oncogenes and tumor suppressor genes, including the key oncogene KIT. Our study identified the presence of KIT, along with other genes such as ERBB2, PDGFRA, MET, FGFR2, and FGFR3, in various components of the PI3K/Akt pathway. These include PI3K/Akt act, PI3K/AKT sig-can, PI5P, PP2A, IER3 reg of PI3K/Akt sig, and Neg. reg. PI3K/AKT net, accounted for 8.4% (Table 3). Additionally, the highest percentage was attributed to successful therapeutic target proteins at 9.7%, whereas apoptosis and positive apoptosis contributed 0.9%. Moreover, mutations or loss of function of PTEN can disrupt the normal regulation of the PI3K/Akt pathway and contribute to various types of human cancers. ³⁴ Our findings indicate that PTEN is present only in PI3K/Akt act and Neg. reg. PI3K/AKT net.

Table 3.

Distribution of apoptosis, positive apoptosis, negative apoptosis, oncogenes tumor suppressor, and successful therapeutic target in PI3K/AKT pathway-related proteins within zone 2.

PI3K/AKT pathway type	A	P/A	N/A	O	S	T
PI3K/AKT act	1 (1.1%)	1 (1.1%)	0 (0.0%)	7 (7.9%)	1 (1.1%)	8 (9%)
PI3K/AKT sig-can	0 (0.0%)	0 (0.0%)	0 (0.0%)	6 (8.9%)	0 (0.0%)	6 (8.9%)
PI5P, PP2A, IER3 reg. PI3K/AKT sig	1 (1.4%)	1 (1.4%)	0 (0.0%)	7 (9.7%)	0 (0.0%)	7 (9.7%)
Neg. reg. PI3K/AKT net	1 (1.2%)	1 (1.2%)	0 (0.0%)	7 (9.0%)	1 (1.2%)	7 (9.0%)
CD28 dep PI3K/Akt sig	0 (0.0%)	0 (0.0%)	0 (0.0%)	0 (0.0%)	0 (0.0%)	3 (21.4%)
Average percentage	3 (0.9%)	3 (0.9%)	0 (0.0%)	27 (8.4%)	2 (0.6%)	31 (9.7%)

Abbreviations: A, apoptosis; P/A, positive apoptosis; N/A, negative apoptosis; O, oncogenes; S, suppressor gene; T, successful therapeutic target.

Explore the shared functions of various proteins within the PI3K/AKT pathway

Proteins commonly found in the PI3K/Akt pathway play crucial roles in the regulation of various biological functions. We 55 proteins that were present in the entire PI3K/Akt pathway (Table 4). Among these proteins, 26 (47.2%) were considered essential, 51 (92.7%) were involved in signaling, 6 (10.9%) were associated with growth, 7 (12.7%) were related to the cell cycle, 24 (43.6%) were involved in the MAPK cascade, 28 (50.9%) were involved in positive signaling, 4 (7.2%) were involved in negative signaling, and 6 (10.9%) functioned as oncogenes or successful therapeutic targets. These findings indicate a significant concentration of proteins within this specific zone 2 of the PI3K/Akt pathway, suggesting that the proteins identified here have the potential to serve as promising targets for drug development.

Table 4.

Distribution of essential, signaling, growth, cell cycle, positive singling, negative signaling, oncogenes, tumor suppressor and successful therapeutic target in PI3K/AKT -related proteins within zone 2.

PI3K/AKT pathway type	Common proteins	E	S	G	C	M	P/S	N/S	O	SG	T
PI3K/AKT act PI3K/AKT sig-can PI5P, PP2A, IER3 reg. PI3K/AKT sig Neg. reg. PI3K/AKT net	AKT	✓	✓	✗	✗	✓	✓	✗	✗	✗	✗
	ERBB2	✓	✓	✓	✗	✓	✓	✗	✓	✗	✗
	PDGFRA	✓	✓	✗	✗	✓	✓	✗	✓	✗	✓
	MET	✓	✓	✗	✗	✗	✗	✗	✓	✗	✓
	FGFR2	✓	✓	✗	✗	✓	✓	✗	✓	✗	✓
	FGFR3	✓	✓	✗	✗	✓	✓	✗	✓	✗	✗

E, essential; S, signalling; G, growth; C, cell cycle; M, MAPK cascade; P/S, positive signaling; N/S, negative signaling; O, oncogenes; SG, suppressor gene; T, successful therapeutic target.

Finally, the intersection of all components within the PI3K/AKT pathway consisted of 5 proteins: CD80, CD28, PIK3R3, PIK3R2, and CD86. These proteins are involved in various processes, including PI3K/AKT act, PI3K/AKT sig can, PI3K/AKT sig, Neg. reg. PI3K/AKT net, and CD28-dependent PI3K/Akt signaling. All 5 proteins were primarily associated with signaling functions. Specifically, CD28 is also implicated in the cell cycle, whereas CD80 is involved in positive signaling. Furthermore, CD80, CD28, and CD86 are successful therapeutic targets.

Discussion

Recent recognition of the importance of protein-protein interactions in understanding cellular functions and identifying therapeutic targets has paved the way for significant advancements in the field of molecular biology. In this study, we built upon our previous research and delved deeper into the role of protein-protein interactions within the PI3K/Akt pathway, specifically focusing on zone 2, which is enriched with proteins associated with various cellular functions. We mapped 4495 proteins in zone 2 to proteins in the PI3K/AKT pathway and analyzed their involvement in different pathways related to PI3K/AKT activation, signaling, and regulation (Table 1). Our objective is to gain a deeper understanding of the roles played by these proteins.

PI3K/Akt plays a critical role in the regulation of the equilibrium between cell proliferation and cell death. Disruption of this pathway can contribute to cancer initiation and progression. Therefore, targeting this pathway by identifying key proteins is essential for impeding the growth and survival of cancer cells. One of the key findings of this study was the identification of signaling proteins dominate various forms of PI3K/Akt, accounting for 90% of the overall proportion. Positive signaling was closely followed by 43%. Essential proteins, the MAPK cascade, cell cycle, growth, and negative signaling also contributed to the pathway, although to a lesser extent (Table 2).

Proteins play critical roles in cancer networks by acting as either oncogenes that promote cancer development or tumor suppressor genes that inhibit tumor growth. This study identified several genes, including KIT, ERBB2, PDGFRA, MET, FGFR2, and FGFR3, which are involved in various PI3K/Akt pathways, such as activation, signaling in cancer, and regulation. These proteins have important implications for current cancer therapeutic approaches. Each of these proteins has been associated with specific types of cancer, and targeted therapies have been developed to inhibit their activity and signaling pathways. Furthermore, they have important implications as therapeutic targets in current cancer therapeutic approaches. Targeted therapies against these genes have shown promising results in certain types of cancer. For example, imatinib has shown efficacy against KIT-mutant cancers, ³⁵ and HER2-targeted therapy has successfully treated HER2-enhanced breast and other cancers. ³⁶ Furthermore, inhibitors targeting PDGFRA, MET, FGFR2, and FGFR3 hold great potential for personalized cancer therapeutic strategies.

Furthermore, this study highlights the presence of successful therapeutic target proteins, accounting for 9.7%, indicating their potential for drug development. The study also mentioned the involvement of apoptosis and positive apoptosis in the pathway, contributing 0.9% to the identified types. Additionally, mutations or loss of function in PTEN can disrupt the normal regulation of the PI3K/AKT pathway and contribute to various types of human cancers. Notably, PTEN is only present in PI3K/AKT act and Neg. reg. PI3K/AKT net, based on these findings. These results suggest that there is a notable accumulation of proteins in zone 2 of the PI3K/AKT pathway. This discovery indicated that some of the proteins found in this area could be valuable candidates for drug development.

This study identified 55 proteins that are commonly found in the PI3K/Akt pathway, and these proteins play crucial roles in regulating various biological functions. Among these, 47.2% were considered essential, indicating their importance in this pathway. Additionally, 92.7% were involved in signaling, highlighting their role in the transmission cellular signals. Furthermore, 10.9% are associated with growth, 12.7% were related to the cell cycle, and 43.6% were involved in the MAPK cascade. In terms of signaling, 50.9% of proteins contributed to positive signaling, while 7.2% were involved in negative signaling. Moreover, 10.9% of the identified proteins function as oncogenes or successful therapeutic targets, suggesting their potential for drug development. Again, these findings indicate a significant concentration of proteins within zone 2 of the PI3K/Akt pathway, highlighting the importance of this specific zone and its potential for targeting specific proteins for therapeutic purposes.

Finally, the interface of all components within the PI3K/AKT pathway includes 5 proteins, CD80, CD28, PIK3R3, PIK3R2, and CD86, which play critical roles in regulating the immune response and tumor microenvironment. These proteins are involved in many signaling pathways. The main functions of these 5 proteins are related to intracellular signaling. Additionally, the importance of CD28, CD80, and CD86 in current cancer therapeutic approaches revolves around their role in modulating immune responses and their potential for immunotherapeutic intervention. CD28 is the key costimulatory receptor on T cells, while CD80 and CD86 are costimulatory ligands on antigen-presenting cells (APCs). This interaction is essential for T cell activation and proliferation. In cancer therapy, researchers are seeking ways to moderate these interactions to enhance antitumor immune responses. For example, immune checkpoint inhibitors, such as CTLA-4 and PD-1/PD-L1 antibodies, are designed to block inhibitory signals and promote T cell activity against cancer cells. In addition, agonistic antibodies against CD28 have been investigated to enhance T cell activation.^{37 -40}

Conclusions

This study emphasizes the significance of protein-protein interactions within the PI3K/Akt pathway, particularly focusing on zone 2 and its enriched proteins associated with various cellular functions. These findings clarify the critical contribution of these proteins in maintaining the delicate balance between cell proliferation and cell death, highlighting the implications of dysregulation in the evolution and dissemination of cancer. By mapping and analyzing the involvement of proteins in different types of the PI3K/Akt pathway, the study identified key proteins dominating the pathway, with signaling proteins being the most prominent. Furthermore, this study identified specific genes and proteins, such as KIT, ERBB2, PDGFRA, MET, FGFR2, FGFR3, CD28, CD80, and CD86, that play essential roles in the activation, signaling, and regulation of the pathway, presenting potential targets for therapeutic interventions and drug development. The concentration of proteins within zone 2 underscores their significance and highlights the possibility of targeting specific proteins for therapeutic purposes. Therefore, these findings contribute to our deeper understanding of protein interactions in the PI3K/Akt pathway and provide valuable insights for future research and development of novel therapeutic strategies against cancer and other related diseases.